/* moldyn main structure */
typedef struct s_moldyn {
int count; /* total amount of atoms */
+ double mass; /* total system mass */
t_atom *atom; /* pointer to the atoms */
t_3dvec dim; /* dimensions of the simulation volume */
t_linkcell lc; /* linked cell list interface */
+ int mean_skip; /* amount of steps without average calc */
+
double t_ref; /* reference temperature */
double t; /* actual temperature */
double t_sum; /* sum over all t */
double ekin; /* kinetic energy */
/* energy averages & fluctuations */
- double k_m;
- double p_m;
- double t_m;
- double dk2_m; /* mean square kinetic energy fluctuations */
- double dp2_m; /* mean square potential energy fluctuations */
- double dt2_m; /* mean square fluctuations in total energy */
+ double k_sum; /* sum of kinetic energy */
+ double v_sum; /* sum of potential energy */
+ double k_mean; /* average of kinetic energy */
+ double v_mean; /* average of potential energy */
+ double k2_sum; /* sum of kinetic energy squared */
+ double v2_sum; /* sum of potential energy squared */
+ double k2_mean; /* average of kinetic energy squared */
+ double v2_mean; /* average of potential energy squared */
+ double dk2_mean; /* mean square kinetic energy fluctuations */
+ double dv2_mean; /* mean square potential energy fluctuations */
/* response functions */
double c_v_nve; /* constant volume heat capacity (nve) */
#define TM_CHI_SIC 0.9776
-#define TM_LC_3C_SIC (0.432e-9*METER) /* A */
+#define TM_LC_SIC 4.32 /* A */
#define ALBE_R_SI (2.82-0.14)
#define ALBE_S_SI (2.82+0.14)
#define ALBE_D_SI 0.81472
#define ALBE_H_SI 0.259
-#define LC_SI_ALBE 5.429
+#define ALBE_LC_SI 5.429
#define ALBE_R_C (2.00-0.15)
#define ALBE_S_C (2.00+0.15)
#define ALBE_D_C 6.28433
#define ALBE_H_C 0.5556
-#define LC_C_ALBE 3.566
+#define ALBE_LC_C 3.566
#define ALBE_R_SIC (2.40-0.20)
#define ALBE_S_SIC (2.40+0.10)
#define ALBE_D_SIC 180.314
#define ALBE_H_SIC 0.68
-#define LC_SIC_ALBE 4.359
+#define ALBE_LC_SIC 4.359
/*
int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
int set_potential_params(t_moldyn *moldyn,void *params);
+int set_mean_skip(t_moldyn *moldyn,int skip);
+
int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);
int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer);
int destroy_atoms(t_moldyn *moldyn);
int thermal_init(t_moldyn *moldyn,u8 equi_init);
+double total_mass_calc(t_moldyn *moldyn);
double temperature_calc(t_moldyn *moldyn);
double get_temperature(t_moldyn *moldyn);
int scale_velocity(t_moldyn *moldyn,u8 equi_init);
double pressure_calc(t_moldyn *moldyn);
+int energy_fluctuation_calc(t_moldyn *moldyn);
+int get_heat_capacity(t_moldyn *moldyn);
double thermodynamic_pressure_calc(t_moldyn *moldyn);
double get_pressure(t_moldyn *moldyn);
int scale_volume(t_moldyn *moldyn);
int moldyn_bc_check(t_moldyn *moldyn);
int get_line(int fd,char *line,int max);
-int calc_fluctuations(double start,double end,t_moldyn *moldyn);
-int get_heat_capacity(t_moldyn *moldyn);
#endif